Signatures of Relaxed Selection in the CYP8B1 Gene of Birds and Mammals

Shinde, Sagar Sharad; Teekas, Lokdeep; Sharma, Sandhya; Vijay, Nagarjun

doi:10.1007/s00239-019-09903-6

Cited by 13 publications

(7 citation statements)

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“…According to previous research, CYP enzymes play a key role in the biotransformation of xenobiotics (alcohol, drugs, carcinogens, and environmental pollutants) and endobiotic compounds (steroids, fatty acids, and bile acids) ( 40 ). Among the DEGs, CYP8B1 plays a vital role in the ratio of primary bile salts, which might provide clues about the evolution of the bile pathway ( 41 ). CYP4A, which consists of 11 subfamilies, is a hydroxylase enzyme that plays a key role in ω-hydroxylation of fatty acids ( 3 ).…”

Section: Discussionmentioning

confidence: 99%

Transcriptome and Gut Microbiota Profiling Analysis of ANIT-Induced Cholestasis and the Effects of Da-Huang-Xiao-Shi Decoction Intervention

Wang

Jiang

et al. 2022

Microbiol Spectr

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Section: Discussionmentioning

confidence: 99%

Transcriptome and Gut Microbiota Profiling Analysis of ANIT-Induced Cholestasis and the Effects of Da-Huang-Xiao-Shi Decoction Intervention

Wang

Jiang

et al. 2022

Microbiol Spectr

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“…In primate species, the potential addition of the extra coding-exon occurs by a shift of the start codon into the untranslated region. Such changes at the reading frame termini occur when the gene is under relaxed selective constraints 59 . Acquisition of novel protein-coding sequences through changes in the exon length is also known to occur 60 .…”

Section: Discussionmentioning

confidence: 99%

Recurrent erosion of COA1/MITRAC15 exemplifies conditional gene dispensability in oxidative phosphorylation

Shinde

Sharma

Teekas

et al. 2021

Sci Rep

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Skeletal muscle fibers rely upon either oxidative phosphorylation or the glycolytic pathway with much less reliance on oxidative phosphorylation to achieve muscular contractions that power mechanical movements. Species with energy-intensive adaptive traits that require sudden bursts of energy have a greater dependency on glycolytic fibers. Glycolytic fibers have decreased reliance on OXPHOS and lower mitochondrial content compared to oxidative fibers. Hence, we hypothesized that gene loss might have occurred within the OXPHOS pathway in lineages that largely depend on glycolytic fibers. The protein encoded by the COA1/MITRAC15 gene with conserved orthologs found in budding yeast to humans promotes mitochondrial translation. We show that gene disrupting mutations have accumulated within the COA1 gene in the cheetah, several species of galliform birds, and rodents. The genomic region containing COA1 is a well-established evolutionary breakpoint region in mammals. Careful inspection of genome assemblies of closely related species of rodents and marsupials suggests two independent COA1 gene loss events co-occurring with chromosomal rearrangements. Besides recurrent gene loss events, we document changes in COA1 exon structure in primates and felids. The detailed evolutionary history presented in this study reveals the intricate link between skeletal muscle fiber composition and the occasional dispensability of the chaperone-like role of the COA1 gene.

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“…Overlapping sets of orthogroups under selection inferred with different analytical approaches, as we resolve here, can therefore implicate consistent, strong, and specific signals of selection. For example, orthogroups with signals of relaxed and diversifying selection likely experienced a release of purifying selection, with the potential for evolutionary diversification [19, 49, 116].…”

Section: Discussionmentioning

confidence: 99%

Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids

2019

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BackgroundSalmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake diversification into morphologically and ecologically distinct variants, often in parallel; these are the lake-resident charr and whitefish (several species in the genera Salvelinus and Coregonus). To identify selection on genes and gene categories associated with such predictable diversifications, we analysed 2702 orthogroups (4.82 Mbp total; average 4.77 genes/orthogroup; average 1783 bp/orthogroup). We did so in two charr and two whitefish species and compared to five other salmonid lineages, which do not evolve in such ecologically predictable ways, and one non-salmonid outgroup.ResultsAll selection analyses are based on Coregonus and Salvelinus compared to non-diversifying taxa. We found more orthogroups were affected by relaxed selection than intensified selection. Of those, 122 were under significant relaxed selection, with trends of an overrepresentation of serine family amino acid metabolism and transcriptional regulation, and significant enrichment of behaviour-associated gene functions. Seventy-eight orthogroups were under significant intensified selection and were enriched for signalling process and transcriptional regulation gene ontology terms and actin filament and lipid metabolism gene sets. Ninety-two orthogroups were under diversifying/positive selection. These were enriched for signal transduction, transmembrane transport, and pyruvate metabolism gene ontology terms and often contained genes involved in transcriptional regulation and development. Several orthogroups showed signs of multiple types of selection. For example, orthogroups under relaxed and diversifying selection contained genes such as ap1m2, involved in immunity and development, and slc6a8, playing an important role in muscle and brain creatine uptake. Orthogroups under intensified and diversifying selection were also found, such as genes syn3, with a role in neural processes, and ctsk, involved in bone remodelling.ConclusionsOur approach pinpointed relevant genomic targets by distinguishing among different kinds of selection. We found that relaxed, intensified, and diversifying selection affect orthogroups and gene functions of ecological relevance in salmonids. Because they were found consistently and robustly across charr and whitefish and not other salmonid lineages, we propose these genes have a potential role in the replicated ecological diversifications.

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Signatures of Relaxed Selection in the CYP8B1 Gene of Birds and Mammals

Cited by 13 publications

References 64 publications

Transcriptome and Gut Microbiota Profiling Analysis of ANIT-Induced Cholestasis and the Effects of Da-Huang-Xiao-Shi Decoction Intervention

Transcriptome and Gut Microbiota Profiling Analysis of ANIT-Induced Cholestasis and the Effects of Da-Huang-Xiao-Shi Decoction Intervention

Recurrent erosion of COA1/MITRAC15 exemplifies conditional gene dispensability in oxidative phosphorylation

Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids

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